Is it normal that SOM clusters the instances with the "versicolor" class into multiple different BMUs?
This is not a bug, assuming you hve implemented the SOM properly with best decay rules of learning rate and neighbourhood strength (in short best hyperparameters). 

Think of the map as finding many local clusters in the Iris-Versicolor class. Since SOM's behave somewhat like k-means clustering, I would say this implies Iris Versicolor has many local clusters which are as closely knit together as the entire classes of Iris setosa and Iris virginica.